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ate-env: update argument ordering for guest operations (#38)
Restructure guest filesystem and shell execution commands in the ate-env
CLI so that the environment ID precedes the operation rather than following
it (e.g. `ate-env <id> read <path>`, `ate-env <id> write <path>`,
`ate-env <id> shell <cmdline>`).
- Keep lifecycle (`create`, `suspend`, `delete`) and `manifest` as top-level commands
- Move persistent `--api` and `--atespace` flags down to subcommands
- Update README.md examples and help output
Fixes #36.